Resonance Energy Transfer Assay with Synaptobrevin Substrate Moiety

ABSTRACT

Compositions and methods for analyzing intracellular BoNT protease activity, and especially BoNT/B, BoNT/G, BoNT/D, and/or BoNT/F protease activity are provided. Most preferably, cells express one or more recombinant hybrid proteins that include one or more fluorescent proteins and at least one BoNT protease recognition and cleavage sequence, and analysis is performed using FRET analysis.

This application claims priority to U.S. provisional application withthe Ser. No. 61/252,315, which was filed Oct. 16, 2009.

FIELD OF THE INVENTION

The field of the invention is Förster resonance energy transfer (FRET)assays for protease activity, especially protease assays for Botulinumneurotoxins BoNTs that cleave synaptobrevin.

BACKGROUND OF THE INVENTION

Botulinum neurotoxins (BoNTs) are extremely toxic proteins and can beclassified into distinct subgroups based, inter alia, on peptidesequence and/or substrate specificity. All of the naturally occurringBoNTs (BoNT/A-G) are composed of a heavy chain that mediates toxin entryinto a target cell and a light chain with zinc-dependent proteaseactivity that hydrolyzes selected SNARE proteins that mediate fusion ofneurotransmitter vesicles to the membrane that forms part of thesynaptic cleft.

For example, the light chain of BoNT/A hydrolyzes with high specificitySNAP-25, which is required for vesicle-mediated exocytosis ofacetylcholine into the synaptic cleft. Known assays for such hydrolyticactivity include those described in our copending Internationalapplication (WO 2009/035476), which is incorporated by reference herein.Here, a fluorophore and a quencher are covalently linked to therespective ends of a peptide sequence that includes, for example, theSNAP-25 sequence. Cleavage by BoNT/A (or other BoNTs with a substratespecificity towards SNAP-25) will result in physical separation of thecleavage products and so reduce fluorescence quenching, which can thenbe quantified. Among other choices, it is often preferred that suchassay is performed as an in vitro solid-phase based assay.

While such assay is conceptually simple and can be used to readilydetermine BoNT/A, BoNT/C, or BoNT/E activity, such assay can not besimply modified to a cell-based assay for determination of BoNT/B,BoNT/D, BoNT/F, or BoNT/G activities by replacing the SNAP-25 motif witha SNARE domain as the SNARE domain includes a membrane spanningsub-domain that would place the N-terminal fluorophore into a vesiclelumen. In such case, only diffusion of the fluorescence signal would beobserved as has been reported elsewhere (Dong et al. PNAS (2004), Vol.101, No. 41, 14701-14706; or U.S. Pat. App. No. 2006/0134722).

Therefore, there is still a need for improved BoNT assays, andespecially cell-based assays for BoNTs that cleave synaptobrevin.

SUMMARY OF THE INVENTION

The present invention is directed to various compositions and methods ofanalyzing BoNT protease activity, and especially BoNT/B, BoNT/G, BoNT/D,and/or BoNT/F protease activity in a cell-based system usingfluorescence resonance energy transfer. Most preferably, the cellsexpress one or more recombinant hybrid proteins together with at leastone BoNT protease recognition and cleavage sequence, wherein the hybridprotein further comprises a transmembrane domain that is not cleavableby the BoNT protease and that directs the hybrid protein to anintracellular synaptic vesicle.

In one aspect of the inventive subject matter, a cell-based method ofmeasuring protease activity of a BoNT protease, in which in one step atransfected cell is provided that produces (I) a hybrid protein having astructure of A-B-C-D or (II) two hybrid proteins having a structure ofA-C-B and A-C-D, respectively, wherein A is a transmembrane domain thatis not cleavable by the BoNT protease, B is a first fluorescent protein,C is a BoNT protease recognition and cleavage sequence, and D is asecond fluorescent protein. IN another step, the transfected cell iscontacted with a BoNT protease under conditions to allow the cell totake up the BoNT protease, and in yet another step, fluorescence ismeasured of at least one of the first and second fluorescent proteins inthe transfected cell.

Most preferably, the transfected cell is a neuronal cell, aneuroendocrine tumor cell, a hybrid cell, or a stem cell. It is furthergenerally preferred that A includes a transmembrane domain fromsynaptobrevin, synaptophysin, synapsin I, synapsin II, and/or synapsinIII, and/or that C includes at least two of a BoNT/B, a BoNT/G, aBoNT/D, and a BoNT/F protease recognition and cleavage sequence. Whilenot limiting to the inventive subject matter, it is further preferredthat a peptide linker is disposed between one or more of A and C, A andB, C and B, and C and D, and that the linker has a length of equal orless than 12 amino acids. Additionally, it is contemplated that thetransfected cell may be contacted with a putative or known BoNTinhibitor prior to contacting the transfected cell with the BoNTprotease. In especially preferred aspects, the transfected cell producestwo hybrid proteins.

In exemplary embodiments, the hybrid protein having the structure ofA-B-C-D has a sequence according to SEQ ID NO:2, the hybrid proteinhaving the structure of A-C-B has a sequence according to SEQ ID NO:4,and the hybrid protein having the structure of A-C-B has a sequenceaccording to SEQ ID NO:6.

Therefore, and viewed from a different perspective, a recombinantnucleic acid includes a sequence that encodes (I) a hybrid proteinhaving a structure of A-B-C-D or (II) two hybrid proteins having astructure of A-C-B and A-C-D, respectively, wherein A is a transmembranedomain that is not cleavable by the BoNT protease, B is a firstfluorescent protein, C is a BoNT protease recognition and cleavagesequence, and D is a second fluorescent protein. Most preferably, Acomprises a transmembrane domain from synaptobrevin, synaptophysin,synapsin I, synapsin II, and/or synapsin III, and/or C comprises atleast two of a BoNT/B, a BoNT/G, a BoNT/D, and a BoNT/F proteaserecognition and cleavage sequence. Where desired, at least oneadditional sequence may be provided that encodes a peptide linker thatis disposed between at least one of A and C, A and B, C and B, and C andD, wherein the linker has a length of equal or less than 12 amino acids.

In especially preferred aspects, the recombinant nucleic acid encodesthe two hybrid proteins. In exemplary nucleic acids, the hybrid proteinhaving the structure of A-B-C-D is encoded by a sequence according toSEQ ID NO:1, the hybrid protein having the structure of A-C-B is encodedby a sequence according to SEQ ID NO:3, and the hybrid protein havingthe structure of A-C-B is encoded by a sequence according to SEQ IDNO:5.

Consequently, the inventors also contemplate a cell transfected with thenucleic acid presented herein, and it is generally preferred that thecell is stably transfected with the nucleic acid. Especially suitablecells include neuronal cells, neuroendocrine tumor cells, hybrid cells,and stem cells. Furthermore, it is typically preferred that the cellcomprises a nucleic acid that encodes the two hybrid proteins having thestructure of A-C-B and A-C-D.

Various objects, features, aspects and advantages of the presentinvention will become more apparent from the following detaileddescription of preferred embodiments of the invention.

BRIEF DESCRIPTION OF THE DRAWING

Prior Art FIGS. 1A-1B are known FRET assays for BoNT protease activityin which two fluorescent proteins are separated by a SNAP25 recognitionand cleavage sequence.

FIGS. 2B-2B are schematic illustrations for intramolecular (2A) andintermolecular (2B) FRET assays for BoNT protease activity according tothe inventive subject matter.

FIGS. 3A-3B are exemplary vector maps for recombinant intramolecular(3A) and intermolecular (3B) FRET constructs according to the inventivesubject matter.

FIG. 4A depicts exemplary FRET results for intramolecular (left panel)and intermolecular (right panel) FRET analysis according to theinventive subject matter.

FIG. 4B is a graphic representation of the results from the experimentsof FIG. 4A.

DETAILED DESCRIPTION

According to the present invention a cell-based FRET assay for BoNT (andespecially for BoNT/B, BoNT/D, BoNT/F, or BoNT/G) is provided in which acell is transfected cell such that the cell produces (a) a single hybridprotein having a structure of A-B-C-D, or (b) two distinct hybridproteins having a structure of A-C-B and A-C-D, respectively, in which Ais a transmembrane domain, B is a first fluorescent protein, C is BoNTprotease recognition and cleavage sequence, and D is a secondfluorescent protein, where most typically, B and D allow for a FRETassay.

It should be appreciated that the hybrid protein(s) that are formed inthe so transfected cells include a transmembrane domain. Therefore,these proteins are expected to locate to intracellular vesicles and toso present a vesicle-bound substrate. Upon exposure of the cells withBoNT, heavy chain-mediated endocytosis of the BoNT into the transfectedcell is followed by presentation of the light chain on the outer surfaceof the vesicle, allowing the protease activity of the light chain tocleave the cleavage sequence of the hybrid protein(s), thus reducingFRET and providing a quantifiable signal. Therefore, it should beappreciated that the compositions and methods presented herein allow fora cell-based assay in which uptake, processing, and proteolytic activitycan be monitored under conditions that closely resemble the naturalconditions.

In contrast, as schematically depicted in Prior Art FIG. 1A, a BoNT/Atest system with a hybrid protein is shown in A. The hybrid protein hasfirst and second fluorescence proteins (CFP and YFP, respectively)covalently coupled to the respective termini of an intermediate peptidesequence that also includes a SNAP-25 sequence (which is the substratefor the BoNT/A light chain protease). Excitation of the CFP results inFRET-mediated fluorescence emission of YFP, thus creating a specificspectral fluorescence signature as schematically illustrated in B. Uponincubation with BoNT/A, the SNAP-25 sequence is hydrolyzed and YFP isreleased from the hybrid molecule (the remainder of which is still boundto a membrane or other solid phase) as depicted in C. Alternatively, oradditionally, excitation and emission may be followed only using YFP,which when separated from the hybrid protein, will ultimately beprocessed in the proteasome complex. Similarly, as shown in Prior ArtFIG. 1B, a hybrid protein has first and second fluorescence proteins(CFP and YFP, respectively) covalently coupled to the respective terminiof an intermediate peptide sequence that also includes a SNAP-25sequence. The hybrid protein is associated to the outside of the vesiclevia the cysteine rich domain of the SNAP-25 sequence. Once more, uponcleavage of the SNAP-25 linker between the CFP and YFP, FRET is nolonger available and fluorescence can be measured either as loss in FRETor ultimately loss in YFP as described above.

While such systems provide various advantages, it should be readilyapparent that that where the SNAP-25 sequence is replaced by asynaptobrevin (VAMP), the presence of the transmembrane sub-domain insynaptobrevin will lead to physical separation of the CFP and YFP by thevesicle (or other) membrane, thus abolishing any FRET between the CFPand YFP as is shown in FIG. 9B of U.S. Pat. App. No. 2006/0134722.

To overcome these difficulties, the inventors now have prepared hybridmolecules suitable for intramolecular FRET in which one fluorescentprotein (or other reporter) is positioned between the transmembranesub-domain and the BoNT protease recognition and cleavage sequence, andwherein another fluorescent protein (or other reporter) is positionedfollowing the BoNT protease recognition and cleavage sequence.Additionally, the inventors have also prepared pairs of hybrid moleculessuitable for intermolecular FRET in which both hybrid molecules have arespective fluorescent protein coupled to respective sequences thatinclude a transmembrane domain and a BoNT protease recognition andcleavage sequence.

As used herein, the term “transmembrane domain” refers to any molecularmoiety that is capable of insertion into a plasma membrane in a mannersuch that at least a portion of the moiety extends into (and moretypically across) the lipid bilayer. Thus, a moiety that only externallycontacts (e.g., via ionic or electrostatic interaction) the outersurface of the plasma membrane is not considered a transmembrane domainunder the definition provided herein. Thus, especially preferredtransmembrane domains include hydrophobic polypeptide domains thatextend into (and more typically across) the plasma membrane. Mosttypically, preferred transmembrane domains comprise a (typicallyrecombinant) polypeptide. However, it should be recognized that variousalternative elements (e.g., N-terminal palmitoylation) will also fallwithin the scope of the definition provided herein.

As also used herein, the term “BoNT recognition and cleavage sequence”refers to any molecular moiety that can be bound and cleaved by a BoNTprotease. It is generally preferred that the BoNT recognition andcleavage sequence comprises a synaptobrevin polypeptide or portionthereof, which is typically a recombinant polypeptide.

In one especially preferred aspect of the inventive subject matter,contemplated recombinant nucleic acids may include a sequence thatencodes (I) a hybrid protein having a structure of A-B-C-D or (II) atleast one of two hybrid proteins having a structure of A-C-B and havinga structure of A-C-D, respectively, where A is a transmembrane domain, Bis a first fluorescent protein, C is a BoNT recognition and cleavagesequence, and D is a second fluorescent protein. Most preferably, wherethe sequence encodes two hybrid proteins, expression of the two hybridproteins is under the control of respective promoters (typically, butnot necessarily, having the same strength and same regulatory controlmechanism).

Most typically, the transmembrane domain is selected such as to allowinsertion of the recombinant protein(s) into the membrane of synapticvesicles. Therefore, it is generally preferred that the transmembranedomain is the transmembrane domain of synaptobrevin, synaptophysin,synapsin I, synapsin II, and/or synapsin III, or any portion thereofthat still confers anchoring of the recombinant protein into themembrane. However, in alternative aspects of the inventive subjectmatter, it is contemplated that various other transmembrane domains arealso deemed suitable so long as such domains will anchor the recombinantprotein to one or more intracellular membranes. There are numeroustransmembrane domains known in the art, and all of those are deemedsuitable for use herein. The person of ordinary skill in the art willreadily be able to identify a domain as a transmembrane domain (e.g.,via publication and description of the domain, or via computationaldomain analysis). Of course, suitable domains naturally occurringdomains as well as mutated forms thereof (e.g., forms with one or moretransitions, transversions, insertions, deletions, inversions, etc.).Moreover, additionally contemplated transmembrane domain may also beentirely synthetic and based on computational analysis.

Similarly, it should be appreciated that the transmembrane domain mayalso be replaced by another polypeptide moiety that allows at leasttemporary anchoring of the hybrid protein to a membrane such that theremainder of the hybrid protein is exposed to the cytosol. Anchoring maybe mediated by various (typically non-covalent) interactions, includingionic, hydrophobic, and/or electrostatic interactions. Still furthercontemplated transmembrane domains also include non-proteintransmembrane domains. For example, especially preferred alternativetransmembrane domains will include those in which a hydrophobic group(e.g., sterol, hydrocarbon, etc.) is attached to the protein, andparticularly a palmitoyl group. Such groups may be added intracellularly(e.g., via palmitoylation signal) or in vitro using various syntheticschemes.

It should further be appreciated that suitable transmembrane domainswill preferably not include a BoNT protease cleavage site and/or a BoNTprotease recognition site and thus only be acting as a transmembraneanchor for the recombinant protein. Therefore, suitable transmembranedomains may include full-length (or substantially full-length)synaptobrevin that has been sufficiently mutated to eliminate thecleavage site and/or recognition site. Alternatively, the synaptobrevin(or other transmembrane domain) may be truncated such that at least thecleavage site and/or recognition site is removed. Moreover, while theabove is directed to single transmembrane domains, it should beappreciated that more than one transmembrane domains are also deemedappropriate (which are preferably coupled to each other via a spacer).

With respect to first and second fluorescent proteins it is generallycontemplated that all known fluorescent proteins are suitable for useherein so long as such proteins can be used as specific and distinctsignal generation moieties. However, it is particularly preferred thatthe signal generation moieties are fluorescent proteins that aresuitable for FRET. For example, first and second fluorescent proteinscan be Cyan Fluorescent Protein (CFP) and Yellow Fluorescent Protein(YFP) and their respective modifications, respectively. Of course, andas already noted above, the fluorescent proteins may be modified toinclude one or more specific characteristics (e.g., spectral) or betruncated to a specific size. Among other choices, contemplatedfluorescent proteins include various blue fluorescent proteins (e.g.,EBFP, EBFP2, Azurite, mKalama1), various cyan fluorescent proteins(e.g., ECFP, Cerulean, CyPet), various green fluorescent proteins (e.g.,AcGFP1, ZsGreen1), and various yellow fluorescent protein derivatives(e.g., YFP, Citrine, Venus, YPet).

Similarly, it should be appreciated that the BoNT protease recognitionand cleavage sequence may vary considerably, so long as such sequence isstill recognized and hydrolyzed by a BoNT light chain. For example, theBoNT protease recognition and cleavage sequence may be of human, rat, ormurine origin, may be present in oligo-multimeric form, and may befurther specifically modified to facilitate or at least partiallyinhibit cleavage. Alternatively, the BoNT protease recognition andcleavage sequence may also be modified to allow identification of one ormore specific BoNT subtypes (e.g., BoNT/B, D, F, and/or G, as welltetanus toxin) by preferential or exclusive cleavage. Of course, itshould be recognized that all isoforms and mutants of BoNT proteaserecognition and cleavage sequences are also deemed suitable for use inconjunction with the teachings presented herein so long as such formsand mutants are also cleavable by one or more BoNT proteases. Forexample, suitable protease recognition and cleavage sequences includethose from VAMP (Synaptobrevin) 1, 2, 3, 4, 5, 6, 7, or 8, and exemplarysequences are listed below where the recognition and cleavage domain isin regular type font, the transmembrane domain is in cursive type font,and where the actual cleavage positions for the respective BoNTproteases are underlined (QK: BoNT/F; KL: BoNT/D; QF: BoNT/B and TeTN;AA: BoNT/G):

Rat Vamp2 Protein sequence (SEQ ID NO: 7): SEQ ID NO: 7MSATAATVPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKNLKMMIILGVICAIILIIII VYFSTMouse Vamp2 Protein sequence (SEQ ID NO: 8): (SEQ ID NO: 8)MSATAATVPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKNLKMMIILGVICAIILIIII VYFSTHuman Vamp2 Protein sequence (SEQ ID NO: 9): (SEQ ID NO: 9)MSATAATAPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKNLKMMIILGVICAIILIIII VYFST

Of course, it should be noted that the above sequences merely serve asexamples for the sequences from which the transmembrane domain and theBoNT protease recognition and cleavage sequences can be obtained from.Thus, it is also noted that numerous alternative sequences other thansynaptobrevin are also contemplated particularly if they can be cleavedby a naturally occurring or a synthetic or designer BoNT, includingSNAP-25 and mutant forms thereof.

It should further be appreciated that one or more of the transmembranedomain, the first and second fluorescent proteins, and the BoNT proteaserecognition and cleavage domain may be truncated while retaining therespective function (i.e., transmembrane anchor, fluorescence, BoNTprotease recognition and cleavage). Moreover, it should be appreciatedthat one or more amino acids in the above elements may be deleted orreplaced by one or more other amino acids, typically in a conservedfashion.

Moreover, it is especially contemplated that the additional amino acidsmay be added as spacers between one or more of the transmembrane domain,the first and second fluorescent proteins, and the BoNT proteaserecognition and cleavage domain. Such spacers may be included to providefurther steric flexibility, increase distance between the elements, etc.Typically, suitable spacers will have a length of between 1-100 aminoacids, more typically between 2-50 amino acids, and most typicallybetween 3-12 amino acids. Where the recombinant protein is used for FRETassays, shorter spacers are generally preferred. Still further, it isnoted that additional domains may be provided to impart further desiredfunctions. For example, suitable additional domains will includeaffinity tags for ease of isolation or antibody-based labeling, celltrafficking to direct the recombinant protein into a desiredcompartment, etc.

With respect to the transfected cells expressing the hybrid protein itis generally preferred that the cell is stably transfected.Nevertheless, transient transfection is also contemplated. There arenumerous promoter structures known in the art, and all of those aregenerally deemed suitable for use herein. However, it is especiallypreferred that the expression is inducible from the promoter. In furthercontemplated aspects, expression may also be constitutively. FIG. 3Adepicts an exemplary vector map for an expression construct of a hybridprotein having a structure of A-B-C-D, and FIG. 3B depicts an exemplaryvector map for expression of two hybrid proteins having a structure ofA-C-B and A-C-D, respectively.

Particularly preferred cells for transfection include neuronal cells(e.g., astrocytes, dendrocytes, glia cells, etc.) and stem cells (e.g.,adult pluripotent, or adult germ line layer, or adult progenitor).However, numerous other non-neuronal cells, including human, rodent,insect cells, and even yeast and bacterial cells are also contemplatedherein.

Consequently, the inventors contemplate a cell-based method of measuringprotease activity of a BoNT protease in which in one step a transfectedcell is provided that produces (I) a hybrid protein having a structureof A-B-C-D or (II) two hybrid proteins having a structure of A-C-B andA-C-D, respectively, wherein A is a transmembrane domain, B is a firstfluorescent protein, C is a BoNT recognition and cleavage sequence, andD is a second fluorescent protein. In exemplary aspects of the inventivesubject matter, the hybrid protein having a structure of A-B-C-D has asequence according to SEQ ID NO:2, which is preferably encoded by anucleic acid having sequence according to SEQ ID NO:1. Where the hybridproteins have a structure of A-C-B and A-C-D, the protein sequences willpreferably be as shown in SEQ ID NO:4 and SEQ ID NO:6, which arepreferably encoded by a nucleic acid having sequence according to SEQ IDNO:3 and SEQ ID NO:5, respectively. Of course, and as already notedearlier, all mutant forms of the above sequences are also expresslycontemplated herein, so long as such mutant forms retain the respectivefunctions as noted above. In another step, the transfected cell iscontacted with a BoNT protease under conditions to allow the cell totake up the BoNT protease, and in yet another step, fluorescence ismeasured from at least one of the first and second fluorescent proteinsin the transfected cell.

Depending on the particular requirements and conditions, contemplatedcell based assays may be performed as depicted in FIG. 2A in which thehybrid protein is a single polypeptide chain having an N-terminaltransmembrane domain, followed by a CFP, which is in turn followed by aBoNT protease recognition and cleavage sequence, which is in turnfollowed by a (preferably terminal) YFP. Expression of the hybridprotein and subsequent translocation of the hybrid protein to themembrane of an intracellular vesicle will result in the presentation ofthe hybrid protein on the outside of the vesicle. The protease activityof BoNT/B will then intracellularly cleave the cleavage sequence, thusreleasing the YFP from the hybrid protein. Consequently, quenching isreduced and fluorescence of the YFP is detectable in diffused form fromthe cell.

Alternatively, as shown in FIG. 2B, two separate hybrid proteins areformed in the cell, each having an N-terminal transmembrane domain,followed by a BoNT protease recognition and cleavage sequence, which isin turn followed by a (preferably terminal) YFP and CFP, respectively.Expression of the hybrid proteins and subsequent translocation of thehybrid proteins to the membrane of an intracellular vesicle will resultin the presentation of the hybrid proteins on the outside of thevesicle. The protease activity of BoNT/B will then intracellularlycleave the cleavage sequences, thus releasing YFP and CFP from thehybrid protein. Consequently, quenching is reduced and fluorescence ofthe YFP and CFP is detectable in diffused form from the cell.Remarkably, the respective hybrid proteins co-locate on the vesicularmembrane in such a manner as to allow for FRET. Exemplary results forsuch assays are depicted in the calculated fluorescence microphotographsof FIG. 4A and the corresponding bar graph representations of FIG. 4B.As can be readily taken from these figures, the FRET assay performedwell in the intermolecular FRET assay and less satisfactorily in theintramolecular FRET assay. However, it is expected that routineexperimentation will also provide satisfactory intramolecular FRET assayresults.

Examples Cloning of Intramolecular Construct

The intramolecular FRET construct, pMD0031 (FIG. 3A), was constructed inpEGFP-C1 (Clontech, Mountain View, Calif.). Three DNA fragments—anN-terminal fragment of rat Vamp2 from the start to amino acid 92, fulllength YFP without a stop codon, and a C-terminal fragment of rat Vamp2from amino acid 93 to the stop—were amplified by polymerase chainreaction (PCR). An EcoRI restriction site was engineered onto the 5′ endof the N-terminal Vamp2 fragment and a SerGlyGly (TCGGGAGGC) linker andthe first 12 nucleotides of the YFP were engineered onto the 3′ end. TheYFP fragment had the last 13 nucleotides of the N-terminal Vamp2fragment and the same SerGlyGly linker as the N-terminal Vamp2 fragmentengineered onto the 5′ end and a second SerGlyGly (AGCGGCGGT) linker andthe first 9 nucleotides of the C-terminal Vamp2 fragment engineered ontothe 3′ end. The C-terminal Vamp2 fragment had the last 12 nucleotides ofYFP without a stop and the same SerGlyGly linker as the YFP fragmentengineered onto the 5′ end and a BamHI restriction site engineered ontothe 3′ end.

These three fragments were then combined using splice overlap extension(SOE) PCR to create a single fragment consisting of an EcoRI restrictionsite, the N-terminal fragment of rat Vamp2 (amino acids 1-92), aSerGlyGly linker, YFP without a stop, a second SerGlyGly linker, theC-terminal fragment of rat Vamp2 (amino acids 93-stop), and an BamHIrestriction site. This fragment and pECFP-C1 were then digested withEcoRI and BamHI, ligated together, and transformed into DH5α E. coli.The final construct insert was then fully sequenced.

Cloning of Intermolecular Construct

The intermolecular FRET construct, pMD0034 (FIG. 3B), was constructed inpBudCE4.1 (Invitrogen, Carlsbad, Calif.). The YFP rat Vamp2 fusion wasgenerated by amplifying two fragments by PCR. The first fragment was YFPwithout a stop with an engineered HindIII restriction site on the 5′ endand a SerGlyGly linker (AGTGGAGGC) and the first 9 nucleotides of ratVamp2 engineered on the 3′ end. The second fragment was full length ratVamp2 with the last 9 nucleotides of YFP and the same SerGlyGly linkerengineered onto the 5′ end and an XbaI restriction site engineered ontothe 3′ end. These two fragments were then combined using SOE PCR tocreate a YFP, SerGlyGly linker, full length Vamp2 fragment. The fragmentand pBudCE4.1 was then digested with HindIII and XbaI, ligated together,and transformed into DH5 α E. coli. The CFP rat Vamp2 fusion was createdsimilarly but contained a CFP without a stop, a NotI restriction site onthe 5′ end, and a KpnI site on the 3′ end. The final construct was thenfully sequenced.

Cell Culture and FRET Assay

Analysis of FRET efficiency, YFP/CFP fluorescence ratios, and BoNT/Bsensitivities of the BoNT/B reporters was performed in cells in vitro.More specifically, Neuro2A cells were grown in a 96-well plate to 70%confluency (2000 cells/well) and transiently transfected usingLipofectamine 2000 (Invitrogen), with the intra- or intermolecularBoNT/B reporters. After 24 h, cells were incubated in the presence orabsence of 25 nM BoNT/B at 37° C. for 72 h in 100 μl of phenol red-freeMEM medium.

Semi-automated FRET or total YFP and CFP fluorescence measurements wereperformed using a Nikon TE2000-U fluorescent microscope with 200×magnification and Nikon NIS Elements 3.4 software. For FRETmeasurements, coefficients-A and -B (acceptor and donor) were calculatedat 0.03 and 0.73 respectively, using a specific bleed-through method.FIG. 4A depicts randomly selected fields pseudo-colored for FRETefficiency or the YFP/CFP fluorescence ratio. YFP/CFP ratios werecalculated from emissions collected upon direct excitement of eachfluorophore. As can be seen from the graphic representation in FIG. 4B,the intermolecular BoNT/B reporter approach was significantly moresensitive for detection of BoNT/B in living cells. 30 randomly selectedcells per condition were analyzed for FRET efficiency (FIG. 4A, leftpanels) or YFP/CFP fluorescence ratios (FIG. 4A, right panels) in thepresence or absence of 25 nM BoNT/B. Indeed, such results were entirelyunexpected as effective intermolecular FRET not only required balancedexpression of the two fluorescent proteins, but also co-location of therecombinant proteins in corresponding quantities. The average signalfrom the 30 cells from 5 microscopic fields on 3 different wells isshown. Cells exhibiting over-saturated fluorescence were excluded.

Thus, specific embodiments and applications of BoNT assays have beendisclosed. It should be apparent, however, to those skilled in the artthat many more modifications besides those already described arepossible without departing from the inventive concepts herein. Theinventive subject matter, therefore, is not to be restricted except inthe spirit of the appended claims.

1. A cell-based method of measuring protease activity of a BoNT protease, comprising: providing a transfected cell that produces (I) a hybrid protein having a structure of A-B-C-D or (II) two hybrid proteins having a structure of A-C-B and A-C-D, respectively; wherein A is a transmembrane domain that is not cleavable by the BoNT protease, B is a first fluorescent protein, C is a BoNT protease recognition and cleavage sequence, and D is a second fluorescent protein; contacting the transfected cell with a BoNT protease under conditions to allow the cell to take up the BoNT protease; and measuring fluorescence of at least one of the first and second fluorescent proteins in the transfected cell.
 2. The method of claim 1 wherein the transfected cell is a cell selected from the group consisting of a neuronal cell, a neuroendocrine tumor cell, a hybrid cell, and a stem cell.
 3. The method of claim 1 wherein A comprises a transmembrane domain from a protein selected form the group consisting of synaptobrevin, synaptophysin, synapsin I, synapsin II, and synapsin III.
 4. The method of claim 1 wherein C comprises at least two of a BoNT/B, a BoNT/G, a BoNT/D, and a BoNT/F protease recognition and cleavage sequence.
 5. The method of claim 1 wherein A and C are portions of synaptobrevin.
 6. The method of claim 1 wherein a peptide linker is disposed between at least one of A and C, A and B, C and B, and C and D, and wherein the linker has a length of equal or less than 12 amino acids.
 7. The method of claim 1 further comprising a step of contacting the transfected cell with a putative BoNT inhibitor prior to the step of contacting the transfected cell with the BoNT protease.
 8. The method of claim 1 wherein the transfected cell produces the two hybrid proteins.
 9. The method of claim 1 wherein the hybrid protein having the structure of A-B-C-D has a sequence according to SEQ ID NO:2, or wherein the hybrid protein having the structure of A-C-B has a sequence according to SEQ ID NO:4, and wherein the hybrid protein having the structure of A-C-B has a sequence according to SEQ ID NO:6.
 10. A recombinant nucleic acid comprising: a sequence that encodes (I) a hybrid protein having a structure of A-B-C-D or (II) two hybrid proteins having a structure of A-C-B and A-C-D, respectively; wherein A is a transmembrane domain that is not cleavable by the BoNT protease, B is a first fluorescent protein, C is a BoNT protease recognition and cleavage sequence, and D is a second fluorescent protein.
 11. The recombinant nucleic acid of claim 10 wherein A comprises a transmembrane domain from a protein selected form the group consisting of synaptobrevin, synaptophysin, synapsin I, synapsin II, and synapsin III.
 12. The recombinant nucleic acid of claim 10 wherein C comprises at least two of a BoNT/B, a BoNT/G, a BoNT/D, and a BoNT/F protease recognition and cleavage sequence.
 13. The recombinant nucleic acid of claim 10 wherein A and C are portions of synaptobrevin.
 14. The recombinant nucleic acid of claim 10 further comprising at least one additional sequence encoding a peptide linker that is disposed between at least one of A and C, A and B, C and B, and C and D, and wherein the linker has a length of equal or less than 12 amino acids.
 15. The recombinant nucleic acid of claim 10 wherein the sequence encodes the two hybrid proteins.
 16. The recombinant nucleic acid of claim 10 wherein the hybrid protein having the structure of A-B-C-D is encoded by a sequence according to SEQ ID NO:1, or wherein the hybrid protein having the structure of A-C-B is encoded by a sequence according to SEQ ID NO:3, and wherein the hybrid protein having the structure of A-C-B is encoded by a sequence according to SEQ ID NO:5.
 17. A cell transfected with the nucleic acid of claim
 10. 18. The cell of claim 17 wherein the cell is stably transfected with the nucleic acid.
 19. The cell of claim 11 wherein the cell is a cell selected from the group consisting of a neuronal cell, a neuroendocrine tumor cell, a hybrid cell, and a stem cell.
 20. The cell of claim 17 wherein the nucleic acid encodes the two hybrid proteins having the structure of A-C-B and A-C-D. 